genomation protocols

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genomation specifications

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Unique identifier OMICS_02306
Name genomation
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.11.13
Stability Stable
Requirements
grid
Maintained Yes

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Maintainers


  • person_outline Christopher E. Mason <>
  • person_outline genomation <>
  • person_outline Altuna Akalin <>
  • person_outline Dirk Schubeler <>

Publication for genomation

genomation in pipelines

 (2)
2018
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] the slim method [] was used to calculate q-values. we used a q-value of less than 0.01 and percent methylation difference larger than 25% as the statistical cutoff for determining dmrs. we used the genomation package [] to classify the dmrs into different genomic regions. genomic coordinates of zebrafish refseq genes, cpg islands and repeat sequences were downloaded from the ucsc genome […]

2017
PMCID: 5487215
PMID: 28653622
DOI: 10.7554/eLife.23203.062

[…] transcription factor binding sites (tfbs), and well positioned nucleosomes was calculated across the 2 kb regions centered on the middle of these regions using the scorematrixbin function in the genomation package () in r (). data were aggregated in 5 bp bins for each region and across all regions covered in a single cell. the average methylation level in pre-defined intervals (dhss, tfbs) […]


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genomation in publications

 (8)
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] the slim method [] was used to calculate q-values. we used a q-value of less than 0.01 and percent methylation difference larger than 25% as the statistical cutoff for determining dmrs. we used the genomation package [] to classify the dmrs into different genomic regions. genomic coordinates of zebrafish refseq genes, cpg islands and repeat sequences were downloaded from the ucsc genome […]

PMCID: 5821458
PMID: 29424686
DOI: 10.7554/eLife.34864.026

[…] in ). read distributions in the region of interest (‘promoters’ and gene ‘bodies’) were visualized in the form of ‘heat’ maps that show scores (coverage) at a given sequence position or bin using genomation package (r, bioconductor) (). for heat maps visualization, paused and non-paused transcripts were further filtered by selecting only those that had overlapping pol 2 peaks […]

PMCID: 5704366
PMID: 29179726
DOI: 10.1186/s12977-017-0378-x

[…] from encode []. genomic coordinates with an associated nucleosome occupancy density signal value greater than zero were used to calculate occupancy matrixes and to plot nucleosome densities with the genomation r package []. bedtools [] and genomation were used to analyze the representation of iss in histone mark distributions [] and in chromatin state segment datasets making use of a consensus […]

PMCID: 5709737
PMID: 29074627
DOI: 10.15252/embj.201797038

[…] and only regions exclusively bound by the individual dnmts were further used to calculate distributions of genomic and epigenomic features, calculate dna methylation, or generate meta‐profiles using genomation in r (akalin et al, )., all datasets produced in this study () have been deposited to the ncbi gene expression omnibus under the accession: gse96529. additional datasets […]

PMCID: 5758878
PMID: 29059365
DOI: 10.1093/nar/gkx951

[…] and raw and mapped data are available at geo (gse89836 and gse103245). the analysis of mapped reads and genomic intervals defined by the bound regions was performed with the genomicranges () and genomation () bioconductor packages., lentiviral vector pgipz (open biosystems) was used to silence the mrna expression of hif1a (v2lhs_132150), epas1 (v2lhs_113753), sin3a (v3lhs_343545) and mxi1 […]


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genomation institution(s)
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia; Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Faculty of Science, University of Basel, Basel, Switzerland; Department of Informatics, University of Oslo, Oslo, Norway
genomation funding source(s)
Supported by the Novartis Research Foundation, the European Union [NoE ‘EpiGeneSys’ FP7- HEALTH-2010-257082 and the ‘Blueprint’ consortium FP7-282510], the European Research Council (EpiGePlas) and the Swiss initiative in Systems Biology (RTD Cell Plasticity), EC Seventh Framework Program [Integra-Life grant 315997], EMBO Young Investigator Program [installation grant 1431/2006] and Croatian MSES [grant 119-0982913-1211].

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